Research workbench
Heterotetrameric glycyl-tRNA synthetase from escherichia COLI
Analyse Heterotetrameric glycyl-tRNA synthetase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EIV
- Type
- protein
- Length
- 1,701 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine--tRNA ligase alpha subunit; Glycine--tRNA ligase beta subunit
- EC
- 6.1.1.14
- UniProt
- P00960, P00961
- Ligands
- ANP, GLY, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) | protein | 299 | 46% helix, 24% strand | P00960 |
| B | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) | protein | 300 | 46% helix, 22% strand | P00960 |
| C | Glycine--tRNA ligase beta subunit (EC 6.1.1.14) | protein | 535 | 49% helix, 15% strand | P00961 |
| D | Glycine--tRNA ligase beta subunit (EC 6.1.1.14) | protein | 567 | 50% helix, 17% strand | P00961 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, C, B, D
- GLY · Glycine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.80 | 0.82 | 102 | MG, ANP, GLY |
| 2 | 279 | 0.78 | 0.90 | 50 | empty |
| 3 | 280 | 0.77 | 0.89 | 47 | empty |
| 4 | 545 | 0.74 | 0.82 | 61 | empty |
| 5 | 527 | 0.73 | 0.82 | 63 | MG, ANP, GLY |
Interfaces
3 interfaces between chains.
- A–B · 2616 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2214 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 2211 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 modified (engineered).
Compared structures
- 7EIV · heterotetrameric glycyl-tRNA synthetase from Escherichia coli · the same entry in another collection · chain B against B, TM-score 1.00
- P00960 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase alpha subunit (P00960) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P00961 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase beta subunit (P00961) · a predicted model of the same protein · chain C against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00960
- Every structure of UniProt P00961
- Elsewhere: RCSB PDB 7EIV · PDBe 7EIV · UniProt P00960 · UniProt P00961
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